Fig. 5: RNMs and TFBSs exhibit differential allelic imbalance.
From: Complex regulatory networks influence pluripotent cell state transitions in human iPSCs
A Density plot showing the allelic imbalance fraction (AIF) of ASCA SNPs in the 13 RNMs. The AIF densities (x-axis) for the 13 RNMs (y-axis) demonstrate that 4 RNMs (indicated by red asterisks) contain ASCA SNPs that have significantly greater allelic imbalance compared to ASCA SNPs in other RNMs (one-sided Mann-Whitney U Test, Benjamini-Hochberg adjusted P-value < 0.05). Source data are provided as a Source Data file. B Histogram showing the number of ASCA SNPs (y-axis) that overlapped predicted TFBSs (x-axis). 6323 SNPs in 4241 ATAC-seq peaks exhibited allele-specific chromatin accessibility (ASCA). ASCA SNPs were intersected with predicted TBFSs for all 92 TF groups. 4299 ASCA SNPs did not overlap a TFBS and 1933 overlapped one or more TFBSs. Source data are provided as a Source Data file. C Barplot demonstrating enrichment for ASCA SNPs in 23 TF groups. A two-tailed Fisher’s Exact test was used to calculate enrichment (Odds Ratio) for ASCA SNPs in the 92 TF groups (Supplementary Data 12). The barplot displays the enrichment (log2(Odds Ratio)) for the 23 TF groups that were significant (adjusted P-value < 0.05). The TF groups are ordered based on their AIF densities in Fig. 5D. Source data are provided as a Source Data file. D Density plot showing the allelic imbalance fraction (AIF) of ASCA SNPs in the 23 TF groups. The AIF densities (x-axis) for the 23 TF groups (y-axis) demonstrate that NANOG-OCT4 Complex binding sites (indicated by red asterisk) contain ASCA SNPs that have greater allelic imbalance compared to ASCA SNPs in the other 22 TF groups (one-sided Mann-Whitney U Test, Benjamini-Hochberg adjusted P-value < 0.05). Source data are provided as a Source Data file.
